JAL-3070 additional interfaces for web services (not yet used!)

diff --git a/src/jalview/ws/api/DistanceMatrixResultI.java b/src/jalview/ws/api/DistanceMatrixResultI.java
new file mode 100644 (file)
index 0000000..a40d256
--- /dev/null
+++ b/src/jalview/ws/api/DistanceMatrixResultI.java
@@ -0,0 +1,16 @@
+package jalview.ws.api;
+
+import jalview.math.MatrixI;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+
+public interface DistanceMatrixResultI
+{
+
+  public MatrixI getDistanceMatrixFor(JobId jobId)
+          throws InvalidArgumentException, ServerError, IOError;
+
+
+}
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diff --git a/src/jalview/ws/api/MsaWithGuideTreeI.java b/src/jalview/ws/api/MsaWithGuideTreeI.java
new file mode 100644 (file)
index 0000000..6c2ff53
--- /dev/null
+++ b/src/jalview/ws/api/MsaWithGuideTreeI.java
@@ -0,0 +1,24 @@
+package jalview.ws.api;
+
+import jalview.analysis.NJTree;
+import jalview.datamodel.SequenceI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.WsParamSetI;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+import java.util.List;
+
+public interface MsaWithGuideTreeI
+{
+  /**
+   * Given a set of sequences
+   * 
+   * @param toalign
+   * @param parameters
+   * @return JobId or exceptions are thrown.
+   */
+  public JobId align(List<SequenceI> toalign, NJTree guideTree,
+          WsParamSetI parameters)
+          throws InvalidArgumentException, ServerError, IOError;
+}
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diff --git a/src/jalview/ws/api/TreeResultI.java b/src/jalview/ws/api/TreeResultI.java
new file mode 100644 (file)
index 0000000..1a0c3bd
--- /dev/null
+++ b/src/jalview/ws/api/TreeResultI.java
@@ -0,0 +1,14 @@
+package jalview.ws.api;
+
+import jalview.analysis.NJTree;
+import jalview.ws.params.InvalidArgumentException;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+
+public interface TreeResultI
+{
+
+  public NJTree getTreeFor(JobId jobId)
+          throws InvalidArgumentException, ServerError, IOError;
+}
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